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Inbreeding reduces long-term growth of Alpine ibex populations

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Many studies document negative inbreeding effects on individuals, and conservation efforts to preserve rare species routinely employ strategies to reduce inbreeding. Despite this, there are few clear examples in nature of inbreeding decreasing the growth rates of populations, and the extent of population-level effects of inbreeding in the wild remains controversial. Here, we take advantage of a long-term dataset of 26 reintroduced Alpine ibex (Capra ibex ibex) populations spanning nearly 100 years to show that inbreeding substantially reduced per capita population growth rates, particularly for populations in harsher environments. Populations with high average inbreeding (F ≈ 0.2) had population growth rates reduced by 71% compared with populations with no inbreeding. Our results show that inbreeding can have long-term demographic consequences even when environmental variation is large and deleterious alleles may have been purged during bottlenecks. Thus, efforts to guard against inbreeding effects in populations of endangered species have not been misplaced.
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Articles
https://doi.org/10.1038/s41559-019-0968-1
1Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland. 2Department of Mathematical Sciences,
Norwegian University of Science and Technology, Trondheim, Norway. 3Department of Integrative Biology, University of Wisconsin-Madison, Madison,
WI, USA. 4Zoological Museum, University of Zurich, Zurich, Switzerland. 5Present address: Wildlife Analysis GmbH, Zurich, Switzerland. 6These authors
contributed equally: Claudio Bozzuto, Iris Biebach. *e-mail: arives@wisc.edu; lukas.keller@ieu.uzh.ch
Inbreeding depression, the harmful effects of inbreeding on the
fitness of individuals, is widespread among plants and animals,
with recent genomic studies revealing an even greater impact
on individual fitness than previously thought1. However, reduced
fitness of individuals due to inbreeding does not necessarily lead
to reduced population growth rates24, in the same way that natu-
ral selection need not impact population growth5. Instead, theory
predicts that the degree to which inbreeding depression affects
population growth will depend on the ecology and life history of a
species3,6. For example, in species experiencing density-dependent
population growth, even substantial inbreeding depression at the
individual level need not translate into reduced population growth,
because fitness reductions caused by inbreeding may be compen-
sated by fitness gains caused by relaxed competition. Under such
circumstances, inbred individuals may produce enough offspring to
maintain population growth (soft selection2).
Collecting unequivocal evidence for population-level effects of
inbreeding is difficult, because it requires many replicated popu-
lations that differ in levels of inbreeding to be monitored over
many generations. Hence, the extent of population-level effects of
inbreeding in the wild remains controversial79, and we currently
lack an understanding of the magnitude of the consequences of
inbreeding depression for long-term population growth in natural
populations10. Here, we take advantage of a long-term dataset of 26
reintroduced Alpine ibex populations (Supplementary Figs. 1 and
2) spanning 23–96 years to show that inbreeding can reduce long-
term population growth rates in the wild.
Alpine ibex were extirpated from the Alps by the end of the
nineteenth century, with only a single population surviving in the
Gran Paradiso region in northern Italy11. Starting in 1906, Alpine
ibex were taken from Gran Paradiso, bred in Swiss zoos and then
released back into their former habitat. These reintroductions are
well documented12, with counts of the released individuals, sub-
sequent time series of annual abundance counts and counts of the
numbers of harvested animals (Supplementary Table 1). Genetic
data suggest little natural migration between populations after rein-
troductions ceased13, making the populations distinct replicates for
the purpose of this study.
The ibex populations in our study experienced up to four rein-
troduction-associated bottlenecks13. The first bottleneck occurred
when the Swiss breeding programme was initiated with ~88 indi-
viduals from Gran Paradiso11. First reintroductions into the wild
with ibex from the Swiss breeding programme caused a second set
of bottlenecks (founder population sizes: 18–78). The third set of
bottlenecks took place when individuals from the first founder pop-
ulations were used to found additional wild populations (founder
population sizes: 9–137). Subsequent reintroductions sourced some
founder individuals from populations that had already experienced
three bottlenecks, thus causing a fourth bottleneck13. Genetically,
the bottlenecks were twice as pronounced as expected from the
number of released founders because, on average, only about half of
the founders contributed genes to the following generations14.
These serial bottlenecks resulted in considerable genetic drift
and inbreeding15. In this study, we use the term inbreeding to refer
to the average identity by descent across individuals that accumu-
lates under random mating in a population of finite size in con-
cert with genetic drift16,17. We quantified this inbreeding using 37
microsatellite loci and population-specific FST estimates that mea-
sure the probability of identity by descent of pairs of alleles at a
locus within populations relative to pairs of alleles from different
populations18,19. Population-specific FST estimates were calculated
for each population individually. Averaged across all populations,
they yield the familiar global FST estimate19. There is no evidence for
inbreeding due to non-random mating within Alpine ibex popula-
tions (FIS 0); therefore, population-specific FST estimates quantify
total inbreeding since the last common ancestral population18,20 at
the beginning of the reintroduction programme about 12.5 genera-
tions ago13. Population-specific FST does not suffer from the same
lack of power as individual inbreeding coefficients estimated from
limited molecular data10,15, because limited dispersal and population
Inbreeding reduces long-term growth of Alpine
ibex populations
Claudio Bozzuto 1,5,6, Iris Biebach 1,6, Stefanie Muff 1,2, Anthony R. Ives 3* and Lukas F. Keller 1,4*
Many studies document negative inbreeding effects on individuals, and conservation efforts to preserve rare species rou-
tinely employ strategies to reduce inbreeding. Despite this, there are few clear examples in nature of inbreeding decreasing
the growth rates of populations, and the extent of population-level effects of inbreeding in the wild remains controversial.
Here, we take advantage of a long-term dataset of 26 reintroduced Alpine ibex (Capra ibex ibex) populations spanning nearly
100 years to show that inbreeding substantially reduced per capita population growth rates, particularly for populations in
harsher environments. Populations with high average inbreeding (F 0.2) had population growth rates reduced by 71% com-
pared with populations with no inbreeding. Our results show that inbreeding can have long-term demographic consequences
even when environmental variation is large and deleterious alleles may have been purged during bottlenecks. Thus, efforts to
guard against inbreeding effects in populations of endangered species have not been misplaced.
NATURE ECOLOGY & EVOLUTION | VOL 3 | SEPTEMBER 2019 | 1359–1364 | www.nature.com/natecolevol 1359
Content courtesy of Springer Nature, terms of use apply. Rights reserved

Supplementary resource (1)

... Genetic diversity will decline in populations subject to reductions in size and increased isolation through genetic drift, increased inbreeding, and reduced gene flow (Schlaepfer et al., 2018;Wright, 1931). These genetic changes can occur rapidly in low vagility species with small populations and can contribute to extinction risks (Bozzuto et al., 2019;Gilpin & Soulé, 1986;Saccheri et al., 1998;Spielman et al., 2004). Genetic sampling can help identify populations with low or declining genetic diversity for management and enhancement. ...
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... An alpine species with currently low genetic diversity, high mutation load, high levels of inbreeding and signs of inbreeding depression, is the Alpine ibex (Capra ibex) (Biebach & Keller, 2009;Bozzuto et al., 2019;Brambilla et al., 2018;Grossen et al., 2018;Grossen et al., 2020). Historic records suggest that Alpine ibex were intensely hunted, presumably since the 15th century and encountered their most severe bottleneck in the 19th century. ...
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Population bottlenecks can have dramatic consequences for the health and long‐term survival of a species. Understanding of historic population size and standing genetic variation prior to a contraction allows estimating the impact of a bottleneck on the species genetic diversity. Although historic population sizes can be modelled based on extant genomics, uncertainty is high for the last 10‐20 millenia. Hence, integrating ancient genomes provides a powerful complement to retrace the evolution of genetic diversity through population fluctuations. Here, we recover 15 high‐quality mitogenomes of the once nearly extinct Alpine ibex spanning 8601 BP to 1919 CE and combine these with 60 published modern whole genomes. Coalescent demography simulations based on modern whole genomes indicate population fluctuations coinciding with the last major glaciation period. Using our ancient and historic mitogenomes, we investigate the more recent demographic history of the species and show that mitochondrial haplotype diversity was reduced to a fifth of the pre‐bottleneck diversity with several highly differentiated mitochondrial lineages having co‐existed historically. The main collapse of mitochondrial diversity coincides with elevated human population growth during the last 1‐2 kya. After recovery, one lineage was spread and nearly fixed across the Alps due to recolonization efforts. Our study highlights that a combined approach integrating genomic data of ancient, historic and extant populations unravels major long‐term population fluctuations from the emergence of a species through its near extinction up to the recent past.
... kakapo [85]; rattle snakes [86]; wolves [83]; killer whales [87]), while some studies show that decreased survival and population growth rate are correlated with higher inbreeding and mutation load (e.g. see arctic foxes [88] and alpine ibex [89]). Unfortunately, our understanding of the functional effects of specific mutations and their impacts on fitness in endangered species remains poor. ...
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... Increased inbreeding may be accompanied by population decline in small populations (Bozzuto et al. 2019;Chen et al. 2016;Feng et al. 2019), which can drive populations to extinction (O'Grady et al. 2006;Saccheri et al. 1998;Wright et al. 2007;Niskanen et al. 2020) showed that inbreeding depression in adult sparrows in our study system varied little across years or across the different island environments inhabited by these house sparrows. Hence, the strength of inbreeding depression is similar between populations, but due to harboring more inbred individuals, the relative effect is stronger in smaller populations . ...
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... However, once reduced and fragmented, populations are likely to be recovering with diminished genetic diversity and often face poor genetic connectivity (Frankham, 1996). This was the case for the Alpine ibex (Capra ibex ibex) that underwent stepwise re-introductions from very small founder populations that had been subjected to serial bottleneck events (Biebach & Keller, 2010) and where high levels of inbreeding are reducing long-term population growth (Bozzuto et al., 2019). Aside from human interventions, species often naturally restore their population sizes as they disperse and recolonize previously inhabited territories (Sommer & Nadachowski, 2006). ...
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Inbreeding depression, the reduction of fitness caused by inbreeding, is a nearly universal phenomenon that depends on past mutation, selection, and genetic drift. Recent estimates suggest that its impact on individual fitness is even greater than previously thought. Genomic information is contributing to its detection and can enlighten important aspects of its genetic architecture. In natural populations, purging and genetic rescue mitigate fitness decline during inbreeding periods, and might be critical to population survival, thus, both mechanisms should be considered when assessing extinction risks. However, deliberate purging and genetic rescue involve considerable risk in the short and medium term, so that neither appears to be a panacea against high inbreeding depression.
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Chapter
In the arguments in Chapter 3 leading to the Hardy-Weinberg principle, we found that, in order to obtain the actual genic structure sg, or genotypic structure Sg, of the population in a future generation g, we had to assume that the population was “infinitely” large.